We do still discourage the Brave Flatpak, mainly because it is not distributed by Brave themselves.
I think as far as sandboxing goes, our conclusion is that the difference it makes is not really enough to actively discourage browser Flatpaks as a whole, so we just note the difference and leave it up to you to decide. I don’t think a decision either way will impact ordinary users. This is why we don’t have the same warning on the Firefox Flatpak for example.